1. Prediction of NO Oxidizable Cysteines Larry Grant Dr. Jamil Momand Cal State L.A.

2. S-nitrosylation Redox-based protein regulation. Redox-based protein regulation. similar to phosphorylation. similar to phosphorylation. reversible reversible detectable detectable Plays a major role in many physiological processes. Plays a major role in many physiological processes. inflammation, cell channel signaling, protease activity inflammation, cell channel signaling, protease activity

3. COPP Project Cysteine Oxidation Prediction Program Cysteine Oxidation Prediction Program Will be web-based Will be web-based Capable of predicting cysteine reactivity based on primary sequence and/or structure data. Capable of predicting cysteine reactivity based on primary sequence and/or structure data. 4 kinds of reactivity 4 kinds of reactivity

4. COPP Algorithm

5. My Project Generate parameters based on sequence information to predict NO susceptibility. Generate parameters based on sequence information to predict NO susceptibility. Stamler et, al have proposed a short motiff based on 27 sequences. Stamler et, al have proposed a short motiff based on 27 sequences. (Lys,Arg,His,Asp,Glu) – Cys – (Asp/Glu) (Lys,Arg,His,Asp,Glu) – Cys – (Asp/Glu)

6. -20………-10…………..-1C+1….…+10……...…+20 Extracting parameters… Data Mining Data Mining Target of 100-150 oxidizable thiols Target of 100-150 oxidizable thiols 71 s-nitrosylated Cys from 63 different proteins. 71 s-nitrosylated Cys from 63 different proteins.

7. PSIPRED Analyzer Three major functions: Average confidence Secondary structure frequency Residue frequency

8. Green = PolarBlue = Basic Black = HydrophobicRed = Acidic H H H H C C C C C C 6 6 6 6 6 6 6 66 6

9. The future Support Vector Machines Support Vector Machines relative solvent accessibility relative solvent accessibility minimum of 1.3 Å 2 minimum of 1.3 Å 2 hydrophobicity, acidity, side-chain length hydrophobicity, acidity, side-chain length

10. References Stamler, et al. Neuron. 1997 May;18(5):691-6. Stamler, et al. “(S)NO signals: translocation, regulation, and a consensus motif.” Neuron. 1997 May;18(5):691-6. Sanchez, et al. “Prediction of reversibly oxidized protein cysteine thiols using protein structure properties.” Protein Sci. 2008 Mar;17(3):473-81. Sanchez, et al. “Prediction of reversibly oxidized protein cysteine thiols using protein structure properties.” Protein Sci. 2008 Mar;17(3):473-81. Hess, et al. “Protein S-nitrosylation - Purview and Parameters.” Nat Rev Mol Cell Biol. 2005 Feb;6(2):150-66. Hess, et al. “Protein S-nitrosylation - Purview and Parameters.” Nat Rev Mol Cell Biol. 2005 Feb;6(2):150-66.

11. Acknowledgements Thank you for all of your help: Thank you for all of your help: Dr. Momand Dr. Momand Dr. Sharp Dr. Sharp Dr. Warter-Perez Dr. Warter-Perez Dr. Johnston Dr. Johnston Ronnie Cheng Ronnie Cheng My fellow interns. My fellow interns. Funded by: